Isolation and Characterization of Achromobacter Sp. CX2 From
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Identification of Active Methylotroph Populations in an Acidic Forest Soil
Microbiology (2002), 148, 2331–2342 Printed in Great Britain Identification of active methylotroph populations in an acidic forest soil by stable- isotope probing Stefan Radajewski,1 Gordon Webster,2† David S. Reay,3‡ Samantha A. Morris,1 Philip Ineson,4 David B. Nedwell,3 James I. Prosser2 and J. Colin Murrell1 Author for correspondence: J. Colin Murrell. Tel: j44 24 7652 2553. Fax: j44 24 7652 3568. e-mail: cmurrell!bio.warwick.ac.uk 1 Department of Biological Stable-isotope probing (SIP) is a culture-independent technique that enables Sciences, University of the isolation of DNA from micro-organisms that are actively involved in a Warwick, Coventry CV4 7AL, UK specific metabolic process. In this study, SIP was used to characterize the active methylotroph populations in forest soil (pH 35) microcosms that were exposed 2 Department of Molecular 13 13 13 13 and Cell Biology, to CH3OH or CH4. Distinct C-labelled DNA ( C-DNA) fractions were resolved University of Aberdeen, from total community DNA by CsCl density-gradient centrifugation. Analysis of Institute of Medical 16S rDNA sequences amplified from the 13C-DNA revealed that bacteria related Sciences, Foresterhill, Aberdeen AB25 2ZD, UK to the genera Methylocella, Methylocapsa, Methylocystis and Rhodoblastus had assimilated the 13C-labelled substrates, which suggested that moderately 3 Department of Biological Sciences, University of acidophilic methylotroph populations were active in the microcosms. Essex, Wivenhoe Park, Enrichments targeted towards the active proteobacterial CH3OH utilizers were Colchester, Essex CO4 3SQ, successful, although none of these bacteria were isolated into pure culture. A UK parallel analysis of genes encoding the key enzymes methanol dehydrogenase 4 Department of Biology, and particulate methane monooxygenase reflected the 16S rDNA analysis, but University of York, PO Box 373, YO10 5YW, UK unexpectedly revealed sequences related to the ammonia monooxygenase of ammonia-oxidizing bacteria (AOB) from the β-subclass of the Proteobacteria. -
Exploring Bacteria Diatom Associations Using Single-Cell
Vol. 72: 73–88, 2014 AQUATIC MICROBIAL ECOLOGY Published online April 4 doi: 10.3354/ame01686 Aquat Microb Ecol FREEREE ACCESSCCESS Exploring bacteria–diatom associations using single-cell whole genome amplification Lydia J. Baker*, Paul F. Kemp Department of Oceanography, University of Hawai’i at Manoa, 1950 East West Road, Center for Microbial Oceanography: Research and Education (C-MORE), Honolulu, Hawai’i 96822, USA ABSTRACT: Diatoms are responsible for a large fraction of oceanic and freshwater biomass pro- duction and are critically important for sequestration of carbon to the deep ocean. As with most surfaces present in aquatic systems, bacteria colonize the exterior of diatom cells, and they inter- act with the diatom and each other. The ecology of diatoms may be better explained by conceptu- alizing them as composite organisms consisting of the host cell and its bacterial associates. Such associations could have collective properties that are not predictable from the properties of the host cell alone. Past studies of these associations have employed culture-based, whole-population methods. In contrast, we examined the composition and variability of bacterial assemblages attached to individual diatoms. Samples were collected in an oligotrophic system (Station ALOHA, 22° 45’ N, 158° 00’ W) at the deep chlorophyll maximum. Forty eukaryotic host cells were isolated by flow cytometry followed by multiple displacement amplification, including 26 Thalassiosira spp., other diatoms, dinoflagellates, coccolithophorids, and flagellates. Bacteria were identified by amplifying, cloning, and sequencing 16S rDNA using primers that select against chloroplast 16S rDNA. Bacterial sequences were recovered from 32 of 40 host cells, and from parallel samples of the free-living and particle-associated bacteria. -
Insights Into the Oxidative Degradation of Cellulose by a Copper Metalloenzyme That Exploits Biomass Components
Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components R. Jason Quinlana,1, Matt D. Sweeneya,1, Leila Lo Leggiob, Harm Ottenb, Jens-Christian N. Poulsenb, Katja Salomon Johansenc,2, Kristian B. R. M. Kroghc, Christian Isak Jørgensenc, Morten Tovborgc, Annika Anthonsenc, Theodora Tryfonad, Clive P. Walterc, Paul Dupreed, Feng Xua, Gideon J. Daviese, and Paul H. Waltone aNovozymes, Inc., Davis, CA 95618; bDepartment of Chemistry, University of Copenhagen, 2100 Copenhagen Ø, Denmark; cNovozymes A/S, DK-2880 Bagsværd, Denmark; dDepartment of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QW, United Kingdom; and eDepartment of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom Edited* by Diter von Wettstein, Washington State University, Pullman, WA, and approved August 2, 2011 (received for review April 13, 2011) The enzymatic degradation of recalcitrant plant biomass is one lysis. From this work, it was suggested that GH61s act directly on of the key industrial challenges of the 21st century. Accordingly, cellulose rendering it more accessible to traditional cellulase there is a continuing drive to discover new routes to promote action (11). Moreover, recent genomic sequencing of the brown polysaccharide degradation. Perhaps the most promising approach rot fungi Postia placenta showed a number of GH61 genes in this involves the application of “cellulase-enhancing factors,” such as organism (13–15), indicating the widespread nature of this those from the glycoside hydrolase (CAZy) GH61 family. Here we family of enzymes in cellulose degradation. As such, GH61s show that GH61 enzymes are a unique family of copper-depen- likely hold major potential for industrial decomposition of dent oxidases. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
Achromobacter Buckle Infection Diagnosed by a 16S Rdna Clone
Hotta et al. BMC Ophthalmology 2014, 14:142 http://www.biomedcentral.com/1471-2415/14/142 CASE REPORT Open Access Achromobacter buckle infection diagnosed by a 16S rDNA clone library analysis: a case report Fumika Hotta1†, Hiroshi Eguchi1*, Takeshi Naito1†, Yoshinori Mitamura1†, Kohei Kusujima2† and Tomomi Kuwahara3† Abstract Background: In clinical settings, bacterial infections are usually diagnosed by isolation of colonies after laboratory cultivation followed by species identification with biochemical tests. However, biochemical tests result in misidentification due to similar phenotypes of closely related species. In such cases, 16S rDNA sequence analysis is useful. Herein, we report the first case of an Achromobacter-associated buckle infection that was diagnosed by 16S rDNA sequence analysis. This report highlights the significance of Achromobacter spp. in device-related ophthalmic infections. Case presentation: A 56-year-old woman, who had received buckling surgery using a silicone solid tire for retinal detachment eighteen years prior to this study, presented purulent eye discharge and conjunctival hyperemia in her right eye. Buckle infection was suspected and the buckle material was removed. Isolates from cultures of preoperative discharge and from deposits on the operatively removed buckle material were initially identified as Alcaligenes and Corynebacterium species. However, sequence analysis of a 16S rDNA clone library using the DNA extracted from the deposits on the buckle material demonstrated that all of the 16S rDNA sequences most closely matched those of Achromobacter spp. We concluded that the initial misdiagnosis of this case as an Alcaligenes buckle infection was due to the unreliability of the biochemical test in discriminating Achromobacter and Alcaligenes species due to their close taxonomic positions and similar phenotypes. -
Taxonomy JN869023
Species that differentiate periods of high vs. low species richness in unattached communities Species Taxonomy JN869023 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 JN674641 Bacteria; Bacteroidetes; [Saprospirae]; [Saprospirales]; Chitinophagaceae; Sediminibacterium JN869030 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 U51104 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae; Limnohabitans JN868812 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae JN391888 Bacteria; Planctomycetes; Planctomycetia; Planctomycetales; Planctomycetaceae; Planctomyces HM856408 Bacteria; Planctomycetes; Phycisphaerae; Phycisphaerales GQ347385 Bacteria; Verrucomicrobia; [Methylacidiphilae]; Methylacidiphilales; LD19 GU305856 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Pelagibacteraceae GQ340302 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales JN869125 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae New.ReferenceOTU470 Bacteria; Cyanobacteria; ML635J-21 JN679119 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae HM141858 Bacteria; Acidobacteria; Holophagae; Holophagales; Holophagaceae; Geothrix FQ659340 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; auto67_4W AY133074 Bacteria; Elusimicrobia; Elusimicrobia; Elusimicrobiales FJ800541 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; R4-41B JQ346769 Bacteria; Acidobacteria; [Chloracidobacteria]; RB41; Ellin6075 -
Ice-Nucleating Particles Impact the Severity of Precipitations in West Texas
Ice-nucleating particles impact the severity of precipitations in West Texas Hemanth S. K. Vepuri1,*, Cheyanne A. Rodriguez1, Dimitri G. Georgakopoulos4, Dustin Hume2, James Webb2, Greg D. Mayer3, and Naruki Hiranuma1,* 5 1Department of Life, Earth and Environmental Sciences, West Texas A&M University, Canyon, TX, USA 2Office of Information Technology, West Texas A&M University, Canyon, TX, USA 3Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA 4Department of Crop Science, Agricultural University of Athens, Athens, Greece 10 *Corresponding authors: [email protected] and [email protected] Supplemental Information 15 S1. Precipitation and Particulate Matter Properties S1.1 Precipitation Categorization In this study, we have segregated our precipitation samples into four different categories, such as (1) snows, (2) hails/thunderstorms, (3) long-lasted rains, and (4) weak rains. For this categorization, we have considered both our observation-based as well as the disdrometer-assigned National Weather Service (NWS) 20 code. Initially, the precipitation samples had been assigned one of the four categories based on our manual observation. In the next step, we have used each NWS code and its occurrence in each precipitation sample to finalize the precipitation category. During this step, a precipitation sample was categorized into snow, only when we identified a snow type NWS code (Snow: S-, S, S+ and/or Snow Grains: SG). Likewise, a precipitation sample was categorized into hail/thunderstorm, only when the cumulative sum of NWS codes for hail was 25 counted more than five times (i.e., A + SP ≥ 5; where A and SP are the codes for soft hail and hail, respectively). -
Achromobacter Infections and Treatment Options
AAC Accepted Manuscript Posted Online 17 August 2020 Antimicrob. Agents Chemother. doi:10.1128/AAC.01025-20 Copyright © 2020 American Society for Microbiology. All Rights Reserved. 1 Achromobacter Infections and Treatment Options 2 Burcu Isler 1 2,3 3 Timothy J. Kidd Downloaded from 4 Adam G. Stewart 1,4 5 Patrick Harris 1,2 6 1,4 David L. Paterson http://aac.asm.org/ 7 1. University of Queensland, Faculty of Medicine, UQ Center for Clinical Research, 8 Brisbane, Australia 9 2. Central Microbiology, Pathology Queensland, Royal Brisbane and Women’s Hospital, 10 Brisbane, Australia on August 18, 2020 at University of Queensland 11 3. University of Queensland, Faculty of Science, School of Chemistry and Molecular 12 Biosciences, Brisbane, Australia 13 4. Infectious Diseases Unit, Royal Brisbane and Women’s Hospital, Brisbane, Australia 14 15 Editorial correspondence can be sent to: 16 Professor David Paterson 17 Director 18 UQ Center for Clinical Research 19 Faculty of Medicine 20 The University of Queensland 1 21 Level 8, Building 71/918, UQCCR, RBWH Campus 22 Herston QLD 4029 AUSTRALIA 23 T: +61 7 3346 5500 Downloaded from 24 F: +61 7 3346 5509 25 E: [email protected] 26 http://aac.asm.org/ 27 28 29 on August 18, 2020 at University of Queensland 30 31 32 33 34 35 36 37 38 39 2 40 Abstract 41 Achromobacter is a genus of non-fermenting Gram negative bacteria under order 42 Burkholderiales. Although primarily isolated from respiratory tract of people with cystic Downloaded from 43 fibrosis, Achromobacter spp. can cause a broad range of infections in hosts with other 44 underlying conditions. -
Protein & Peptide Letters
696 Send Orders for Reprints to [email protected] Protein & Peptide Letters, 2017, 24, 696-709 REVIEW ARTICLE ISSN: 0929-8665 eISSN: 1875-5305 Impact Factor: 1.068 Glycan Phosphorylases in Multi-Enzyme Synthetic Processes BENTHAM Editor-in-Chief: SCIENCE Ben M. Dunn Giulia Pergolizzia, Sakonwan Kuhaudomlarpa, Eeshan Kalitaa,b and Robert A. Fielda,* aDepartment of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; bDepartment of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur, Assam -784028, India Abstract: Glycoside phosphorylases catalyse the reversible synthesis of glycosidic bonds by glyco- A R T I C L E H I S T O R Y sylation with concomitant release of inorganic phosphate. The equilibrium position of such reac- tions can render them of limited synthetic utility, unless coupled with a secondary enzymatic step Received: January 17, 2017 Revised: May 24, 2017 where the reaction lies heavily in favour of product. This article surveys recent works on the com- Accepted: June 20, 2017 bined use of glycan phosphorylases with other enzymes to achieve synthetically useful processes. DOI: 10.2174/0929866524666170811125109 Keywords: Phosphorylase, disaccharide, α-glucan, cellodextrin, high-value products, biofuel. O O 1. INTRODUCTION + HO OH Glycoside phosphorylases (GPs) are carbohydrate-active GH enzymes (CAZymes) (URL: http://www.cazy.org/) [1] in- H2O O GP volved in the formation/cleavage of glycosidic bond together O O GT O O + HO O + HO with glycosyltransferase (GT) and glycoside hydrolase (GH) O -- NDP OPO3 NDP -- families (Figure 1) [2-6]. GT reactions favour the thermody- HPO4 namically more stable glycoside product [7]; however, these GS R enzymes can be challenging to work with because of their O O + HO current limited availability and relative instability, along R with the expense of sugar nucleotide substrates [7]. -
Human Milk Microbiota Profiles in Relation to Birthing Method, Gestation and Infant Gender Camilla Urbaniak1,2, Michelle Angelini3, Gregory B
Urbaniak et al. Microbiome (2016) 4:1 DOI 10.1186/s40168-015-0145-y RESEARCH Open Access Human milk microbiota profiles in relation to birthing method, gestation and infant gender Camilla Urbaniak1,2, Michelle Angelini3, Gregory B. Gloor4 and Gregor Reid1,2* Abstract Background: Human milk is an important source of bacteria for the developing infant and has been shown to influence the bacterial composition of the neonate, which in turn can affect disease risk later in life. Very little is known about what factors shape the human milk microbiome. The goal of the present study was to examine the milk microbiota from a range of women who delivered vaginally or by caesarean (C) section, who gave birth to males or females, at term or preterm. Methods: Milk was collected from 39 Caucasian Canadian women, and microbial profiles were analyzed by 16S ribosomal RNA (rRNA) sequencing using the Illumina platform. Results: A diverse community of milk bacteria was found with the most dominant phyla being Proteobacteria and Firmicutes and at the genus level, Staphylococcus, Pseudomonas, Streptococcus and Lactobacillus. Comparison of bacterial profiles between preterm and term births, C section (elective and non-elective) and vaginal deliveries, and male and female infants showed no statistically significant differences. Conclusions: The study revealed the diverse bacterial types transferred to newborns. We postulate that there may be a fail-safe mechanism whereby the mother is “ready” to pass along her bacterial imprint irrespective of when and how the baby is born. Keywords: Human milk, Milk microbiota, Factors affecting the milk microbiota Background levels of Bifidobacterium in human milk correlate with With the incidence of various non-infectious diseases on low levels of Bifidobacterium in the neonatal gut [3], the rise, there is much interest in the developmental ori- allowing for higher than normal levels of Bacteroides to gins of health and disease and the potential role of early be established [4]. -
In Vitro and in Vivo Exploration of the Cellobiose and Cellodextrin Phosphorylases Panel in Ruminiclostridium Cellulolyticum: Im
Liu et al. Biotechnol Biofuels (2019) 12:208 https://doi.org/10.1186/s13068-019-1549-x Biotechnology for Biofuels RESEARCH Open Access In vitro and in vivo exploration of the cellobiose and cellodextrin phosphorylases panel in Ruminiclostridium cellulolyticum: implication for cellulose catabolism Nian Liu1, Aurélie Fosses1, Clara Kampik1, Goetz Parsiegla2, Yann Denis3, Nicolas Vita1, Henri‑Pierre Fierobe1 and Stéphanie Perret1* Abstract Background: In anaerobic cellulolytic micro‑organisms, cellulolysis results in the action of several cellulases gathered in extracellular multi‑enzyme complexes called cellulosomes. Their action releases cellobiose and longer cellodex‑ trins which are imported and further degraded in the cytosol to fuel the cells. In Ruminiclostridium cellulolyticum, an anaerobic and cellulolytic mesophilic bacteria, three cellodextrin phosphorylases named CdpA, CdpB, and CdpC, were identifed in addition to the cellobiose phosphorylase (CbpA) previously characterized. The present study aimed at characterizing them, exploring their implication during growth on cellulose to better understand the life‑style of cellulolytic bacteria on such substrate. Results: The three cellodextrin phosphorylases from R. cellulolyticum displayed marked diferent enzymatic char‑ acteristics. They are specifc for cellodextrins of diferent lengths and present diferent kcat values. CdpC is the most active enzyme before CdpA, and CdpB is weakly active. Modeling studies revealed that a mutation of a conserved histidine residue in the phosphate ion‑binding pocket in CdpB and CdpC might explain their activity‑level diferences. The genes encoding these enzymes are scattered over the chromosome of R. cellulolyticum and only the expression of the gene encoding the cellobiose phosphorylase and the gene cdpA is induced during cellulose growth. Char‑ acterization of four independent mutants constructed in R. -
Microbial Diversity of Soda Lake Habitats
Microbial Diversity of Soda Lake Habitats Von der Gemeinsamen Naturwissenschaftlichen Fakultät der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Susanne Baumgarte aus Fritzlar 1. Referent: Prof. Dr. K. N. Timmis 2. Referent: Prof. Dr. E. Stackebrandt eingereicht am: 26.08.2002 mündliche Prüfung (Disputation) am: 10.01.2003 2003 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Gemeinsamen Naturwissenschaftlichen Fakultät, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Baumgarte, S., Moore, E. R. & Tindall, B. J. (2001). Re-examining the 16S rDNA sequence of Halomonas salina. International Journal of Systematic and Evolutionary Microbiology 51: 51-53. Tagungsbeiträge Baumgarte, S., Mau, M., Bennasar, A., Moore, E. R., Tindall, B. J. & Timmis, K. N. (1999). Archaeal diversity in soda lake habitats. (Vortrag). Jahrestagung der VAAM, Göttingen. Baumgarte, S., Tindall, B. J., Mau, M., Bennasar, A., Timmis, K. N. & Moore, E. R. (1998). Bacterial and archaeal diversity in an African soda lake. (Poster). Körber Symposium on Molecular and Microsensor Studies of Microbial Communities, Bremen. II Contents 1. Introduction............................................................................................................... 1 1.1. The soda lake environment .................................................................................